+++ /dev/null
-/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3
- * of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
- */
-package jalview.datamodel;
-
-import jalview.util.Comparison;
-import jalview.util.MapList;
-
-import java.util.ArrayList;
-import java.util.Iterator;
-import java.util.List;
-import java.util.NoSuchElementException;
-import java.util.Vector;
-
-public class Mapping
-{
- /**
- * An iterator that serves the aligned codon positions (with their protein
- * products).
- *
- * @author gmcarstairs
- *
- */
- public class AlignedCodonIterator implements Iterator<AlignedCodon>
- {
- /*
- * The gap character used in the aligned sequence
- */
- private final char gap;
-
- /*
- * The characters of the aligned sequence e.g. "-cGT-ACgTG-"
- */
- private final SequenceI alignedSeq;
-
- /*
- * the sequence start residue
- */
- private int start;
-
- /*
- * Next position (base 0) in the aligned sequence
- */
- private int alignedColumn = 0;
-
- /*
- * Count of bases up to and including alignedColumn position
- */
- private int alignedBases = 0;
-
- /*
- * [start, end] from ranges (base 1)
- */
- private Iterator<int[]> fromRanges;
-
- /*
- * [start, end] to ranges (base 1)
- */
- private Iterator<int[]> toRanges;
-
- /*
- * The current [start, end] (base 1) from range
- */
- private int[] currentFromRange = null;
-
- /*
- * The current [start, end] (base 1) to range
- */
- private int[] currentToRange = null;
-
- /*
- * The next 'from' position (base 1) to process
- */
- private int fromPosition = 0;
-
- /*
- * The next 'to' position (base 1) to process
- */
- private int toPosition = 0;
-
- /**
- * Constructor
- *
- * @param seq
- * the aligned sequence
- * @param gapChar
- */
- public AlignedCodonIterator(SequenceI seq, char gapChar)
- {
- this.alignedSeq = seq;
- this.start = seq.getStart();
- this.gap = gapChar;
- fromRanges = map.getFromRanges().iterator();
- toRanges = map.getToRanges().iterator();
- if (fromRanges.hasNext())
- {
- currentFromRange = fromRanges.next();
- fromPosition = currentFromRange[0];
- }
- if (toRanges.hasNext())
- {
- currentToRange = toRanges.next();
- toPosition = currentToRange[0];
- }
- }
-
- /**
- * Returns true unless we have already traversed the whole mapping.
- */
- @Override
- public boolean hasNext()
- {
- if (fromRanges.hasNext())
- {
- return true;
- }
- if (currentFromRange == null || fromPosition >= currentFromRange[1])
- {
- return false;
- }
- return true;
- }
-
- /**
- * Returns the next codon's aligned positions, and translated value.
- *
- * @throws NoSuchElementException
- * if hasNext() would have returned false
- * @throws IncompleteCodonException
- * if not enough mapped bases are left to make up a codon
- */
- @Override
- public AlignedCodon next() throws IncompleteCodonException
- {
- if (!hasNext())
- {
- throw new NoSuchElementException();
- }
-
- int[] codon = getNextCodon();
- int[] alignedCodon = getAlignedCodon(codon);
-
- String peptide = getPeptide();
- int peptideCol = toPosition - 1 - Mapping.this.to.getStart();
- return new AlignedCodon(alignedCodon[0], alignedCodon[1],
- alignedCodon[2], peptide, peptideCol);
- }
-
- /**
- * Retrieve the translation as the 'mapped to' position in the mapped to
- * sequence.
- *
- * @return
- * @throws NoSuchElementException
- * if the 'toRange' is exhausted (nothing to map to)
- */
- private String getPeptide()
- {
- // TODO should ideally handle toRatio other than 1 as well...
- // i.e. code like getNextCodon()
- if (toPosition <= currentToRange[1])
- {
- SequenceI seq = Mapping.this.to;
- char pep = seq.getCharAt(toPosition - seq.getStart());
- toPosition++;
- return String.valueOf(pep);
- }
- if (!toRanges.hasNext())
- {
- throw new NoSuchElementException(
- "Ran out of peptide at position " + toPosition);
- }
- currentToRange = toRanges.next();
- toPosition = currentToRange[0];
- return getPeptide();
- }
-
- /**
- * Get the (base 1) dataset positions for the next codon in the mapping.
- *
- * @throws IncompleteCodonException
- * if less than 3 remaining bases are mapped
- */
- private int[] getNextCodon()
- {
- int[] codon = new int[3];
- int codonbase = 0;
-
- while (codonbase < 3)
- {
- if (fromPosition <= currentFromRange[1])
- {
- /*
- * Add next position from the current start-end range
- */
- codon[codonbase++] = fromPosition++;
- }
- else
- {
- /*
- * Move to the next range - if there is one
- */
- if (!fromRanges.hasNext())
- {
- throw new IncompleteCodonException();
- }
- currentFromRange = fromRanges.next();
- fromPosition = currentFromRange[0];
- }
- }
- return codon;
- }
-
- /**
- * Get the aligned column positions (base 0) for the given sequence
- * positions (base 1), by counting ungapped characters in the aligned
- * sequence.
- *
- * @param codon
- * @return
- */
- private int[] getAlignedCodon(int[] codon)
- {
- int[] aligned = new int[codon.length];
- for (int i = 0; i < codon.length; i++)
- {
- aligned[i] = getAlignedColumn(codon[i]);
- }
- return aligned;
- }
-
- /**
- * Get the aligned column position (base 0) for the given sequence position
- * (base 1).
- *
- * @param sequencePos
- * @return
- */
- private int getAlignedColumn(int sequencePos)
- {
- /*
- * allow for offset e.g. treat pos 8 as 2 if sequence starts at 7
- */
- int truePos = sequencePos - (start - 1);
- int length = alignedSeq.getLength();
- while (alignedBases < truePos && alignedColumn < length)
- {
- char c = alignedSeq.getCharAt(alignedColumn++);
- if (c != gap && !Comparison.isGap(c))
- {
- alignedBases++;
- }
- }
- return alignedColumn - 1;
- }
-
- @Override
- public void remove()
- {
- // ignore
- }
-
- }
-
- /*
- * Contains the start-end pairs mapping from the associated sequence to the
- * sequence in the database coordinate system. It also takes care of step
- * difference between coordinate systems.
- */
- MapList map = null;
-
- /*
- * The sequence that map maps the associated sequence to (if any).
- */
- SequenceI to = null;
-
- /*
- * optional sequence id for the 'from' ranges
- */
- private String mappedFromId;
-
- public Mapping(MapList map)
- {
- super();
- this.map = map;
- }
-
- public Mapping(SequenceI to, MapList map)
- {
- this(map);
- this.to = to;
- }
-
- /**
- * create a new mapping from
- *
- * @param to
- * the sequence being mapped
- * @param exon
- * int[] {start,end,start,end} series on associated sequence
- * @param is
- * int[] {start,end,...} ranges on the reference frame being mapped
- * to
- * @param i
- * step size on associated sequence
- * @param j
- * step size on mapped frame
- */
- public Mapping(SequenceI to, int[] exon, int[] is, int i, int j)
- {
- this(to, new MapList(exon, is, i, j));
- }
-
- /**
- * create a duplicate (and independent) mapping object with the same reference
- * to any SequenceI being mapped to.
- *
- * @param map2
- */
- public Mapping(Mapping map2)
- {
- if (map2 != this && map2 != null)
- {
- if (map2.map != null)
- {
- map = new MapList(map2.map);
- }
- to = map2.to;
- mappedFromId = map2.mappedFromId;
- }
- }
-
- /**
- * @return the map
- */
- public MapList getMap()
- {
- return map;
- }
-
- /**
- * @param map
- * the map to set
- */
- public void setMap(MapList map)
- {
- this.map = map;
- }
-
- /**
- * Equals that compares both the to references and MapList mappings.
- *
- * @param o
- * @return
- * @see MapList#equals
- */
- @Override
- public boolean equals(Object o)
- {
- if (o == null || !(o instanceof Mapping))
- {
- return false;
- }
- Mapping other = (Mapping) o;
- if (other == this)
- {
- return true;
- }
- if (other.to != to)
- {
- return false;
- }
- if ((map != null && other.map == null)
- || (map == null && other.map != null))
- {
- return false;
- }
- if ((map == null && other.map == null) || map.equals(other.map))
- {
- return true;
- }
- return false;
- }
-
- /**
- * Returns a hashCode made from the sequence and maplist
- */
- @Override
- public int hashCode()
- {
- int hashCode = (this.to == null ? 1 : this.to.hashCode());
- if (this.map != null)
- {
- hashCode = hashCode * 31 + this.map.hashCode();
- }
-
- return hashCode;
- }
-
-// /**
-// * gets boundary in direction of mapping
-// *
-// * @param position
-// * in mapped reference frame
-// * @return int{start, end} positions in associated sequence (in direction of
-// * mapped word)
-// */
-// public int[] getWord(int mpos)
-// {
-// // BH never called
-// if (map != null)
-// {
-// return map.getToWord(mpos);
-// }
-// return null;
-// }
-
- /**
- * width of mapped unit in associated sequence
- *
- */
- public int getWidth()
- {
- if (map != null)
- {
- return map.getFromRatio();
- }
- return 1;
- }
-
- /**
- * width of unit in mapped reference frame
- *
- * @return
- */
- public int getMappedWidth()
- {
- if (map != null)
- {
- return map.getToRatio();
- }
- return 1;
- }
-
- /**
- * get the 'initial' position in the associated sequence for a position in the
- * mapped reference frame
- *
- * or the mapped position in the associated reference frame for position pos in
- * the associated sequence.
- *
- *
- * @param reg reg[POS]
- * @param isMapped
- *
- * @return position or mapped position
- */
- public int getPosition(int[] reg, boolean isMapped)
- {
- int pos = reg[MapList.POS];
- if (map != null)
- {
- reg = (isMapped ? map.shiftFrom(reg) : map.shiftTo(reg));
- if (reg != null)
- {
- return reg[MapList.POS_TO]; // was newArray[0], but shift puts the result in COUNT_TO
- }
- }
- return pos;
- }
-
-// /**
-//* get mapped position in the associated reference frame for position pos in
-//* the associated sequence.
-// *
-// * @param pos
-// * @return
-// */
-// public int getMappedPosition(int[] reg)
-// {
-// int mpos = reg[MapList.POS];
-// if (map != null)
-// {
-// reg = map.shiftFrom(reg);
-// if (reg != null)
-// {
-// return reg[MapList.POS_TO]; // was newArray[0], but shift puts the result in COUNT_TO
-// }
-// }
-// return mpos;
-// }
-
-// public int[] getMappedWord(int pos)
-// {
-// // BH Not used?
-// if (map != null)
-// {
-// reg = map.shiftFrom(reg);
-// if (reg != null)
-// {
-// reg[MP_0] =
-// return new int[] { mp[0], mp[0] + mp[2] * (map.getToRatio() - 1) };
-// }
-// }
-// return null;
-// }
-
- /**
- * locates the region of feature f in the associated sequence's reference
- * frame
- *
- * @param f
- * @return one or more features corresponding to f
- */
- public SequenceFeature[] locateFeature(SequenceFeature f)
- {
- if (true)
- { // f.getBegin()!=f.getEnd()) {
- if (map != null)
- {
- int[] frange = map.locateInFrom(f.getBegin(), f.getEnd());
- if (frange == null)
- {
- // JBPNote - this isprobably not the right thing to doJBPHack
- return null;
- }
- SequenceFeature[] vf = new SequenceFeature[frange.length / 2];
- for (int i = 0, v = 0; i < frange.length; i += 2, v++)
- {
- vf[v] = new SequenceFeature(f, frange[i], frange[i + 1],
- f.getFeatureGroup(), f.getScore());
- if (frange.length > 2)
- {
- vf[v].setDescription(f.getDescription() + "\nPart " + (v + 1));
- }
- }
- return vf;
- }
- }
-
- // give up and just return the feature.
- return new SequenceFeature[] { f };
- }
-
- /**
- * return a series of contigs on the associated sequence corresponding to the
- * from,to interval on the mapped reference frame
- *
- * @param from
- * @param to
- * @return int[] { from_i, to_i for i=1 to n contiguous regions in the
- * associated sequence}
- */
- public int[] locateRange(int from, int to)
- {
- if (map != null)
- {
- if (from <= to)
- {
- from = (map.getToLowest() < from) ? from : map.getToLowest();
- to = (map.getToHighest() > to) ? to : map.getToHighest();
- if (from > to)
- {
- return null;
- }
- }
- else
- {
- from = (map.getToHighest() > from) ? from : map.getToHighest();
- to = (map.getToLowest() < to) ? to : map.getToLowest();
- if (from < to)
- {
- return null;
- }
- }
- return map.locateInFrom(from, to);
- }
- return new int[] { from, to };
- }
-
- /**
- * return a series of mapped contigs mapped from a range on the associated
- * sequence
- *
- * @param from
- * @param to
- * @return
- */
- public int[] locateMappedRange(int from, int to)
- {
- if (map != null)
- {
-
- if (from <= to)
- {
- from = (map.getFromLowest() < from) ? from : map.getFromLowest();
- to = (map.getFromHighest() > to) ? to : map.getFromHighest();
- if (from > to)
- {
- return null;
- }
- }
- else
- {
- from = (map.getFromHighest() > from) ? from : map.getFromHighest();
- to = (map.getFromLowest() < to) ? to : map.getFromLowest();
- if (from < to)
- {
- return null;
- }
- }
- return map.locateInTo(from, to);
- }
- return new int[] { from, to };
- }
-
- /**
- * return a new mapping object with a maplist modifed to only map the visible
- * regions defined by viscontigs.
- *
- * @param viscontigs
- * @return
- */
- public Mapping intersectVisContigs(int[] viscontigs)
- {
- Mapping copy = new Mapping(this);
- if (map != null)
- {
-// int vpos = 0;
-// int apos = 0;
- List<int[]> toRange = new ArrayList<int[]>();
- List<int[]> fromRange = new ArrayList<int[]>();
- for (int vc = 0; vc < viscontigs.length; vc += 2)
- {
- // find a mapped range in this visible region
- int[] mpr = locateMappedRange(1 + viscontigs[vc],
- viscontigs[vc + 1] - 1);
- if (mpr != null)
- {
- for (int m = 0; m < mpr.length; m += 2)
- {
- toRange.add(new int[] { mpr[m], mpr[m + 1] });
- int[] xpos = locateRange(mpr[m], mpr[m + 1]);
- for (int x = 0; x < xpos.length; x += 2)
- {
- fromRange.add(new int[] { xpos[x], xpos[x + 1] });
- }
- }
- }
- }
- int[] from = new int[fromRange.size() * 2];
- int[] to = new int[toRange.size() * 2];
- int[] r;
- for (int f = 0, fSize = fromRange.size(); f < fSize; f++)
- {
- r = fromRange.get(f);
- from[f * 2] = r[0];
- from[f * 2 + 1] = r[1];
- }
- for (int f = 0, fSize = toRange.size(); f < fSize; f++)
- {
- r = toRange.get(f);
- to[f * 2] = r[0];
- to[f * 2 + 1] = r[1];
- }
- copy.setMap(
- new MapList(from, to, map.getFromRatio(), map.getToRatio()));
- }
- return copy;
- }
-
- /**
- * get the sequence being mapped to - if any
- *
- * @return null or a dataset sequence
- */
- public SequenceI getTo()
- {
- return to;
- }
-
- /**
- * set the dataset sequence being mapped to if any
- *
- * @param tto
- */
- public void setTo(SequenceI tto)
- {
- to = tto;
- }
-
- /**
- * Returns an iterator which can serve up the aligned codon column positions
- * and their corresponding peptide products
- *
- * @param seq
- * an aligned (i.e. possibly gapped) sequence
- * @param gapChar
- * @return
- */
- public Iterator<AlignedCodon> getCodonIterator(SequenceI seq,
- char gapChar)
- {
- return new AlignedCodonIterator(seq, gapChar);
- }
-
- /**
- * Readable representation for debugging only, not guaranteed not to change
- */
- @Override
- public String toString()
- {
- return String.format("%s %s", this.map.toString(),
- this.to == null ? "" : this.to.getName());
- }
-
- /**
- * Returns the identifier for the 'from' range sequence, or null if not set
- *
- * @return
- */
- public String getMappedFromId()
- {
- return mappedFromId;
- }
-
- /**
- * Sets the identifier for the 'from' range sequence
- */
- public void setMappedFromId(String mappedFromId)
- {
- this.mappedFromId = mappedFromId;
- }
-
-}
git://source.jalview.org / jalview.git / blobdiff